Merge branch 'main' into custom_lsoda_call

1 files changed, 29 insertions, 29 deletions

diff --git a/log/test.log b/log/test.log
index 10c0aa76..dc1b6c74 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,57 +1,57 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [2.9s]
+✔ |         5 | Analytical solutions for coupled models [1.6s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [29.5s]
+✔ |        12 | Confidence intervals and p-values [0.4s]
+✔ |     1  12 | Dimethenamid data from 2018 [12.4s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_dmta.R:99'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Skip ('test_dmta.R:98'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [4.9s]
+✔ |        14 | Error model fitting [2.3s]
 ✔ |         5 | Time step normalisation
-✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
-✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
-✔ |         1 | Fitting the logistic model [0.2s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [24.7s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
+✔ |         4 | Calculation of FOCUS chi2 error levels [0.3s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.2s]
+✔ |         1 | Fitting the logistic model [0.1s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s]
+✔ |     1  11 | Nonlinear mixed-effects models [5.9s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits
+Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.5s]
-✔ |         3 | mkinfit features [0.7s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.4s]
-✔ |         7 | Multistart method for saem.mmkin models [36.8s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.5s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.8s]
-✔ |        16 | Plotting [10.0s]
+✔ |        10 | Special cases of mkinfit calls [0.4s]
+✔ |         3 | mkinfit features [0.5s]
+✔ |         8 | mkinmod model generation and printing
+✔ |         3 | Model predictions with mkinpredict [0.1s]
+✔ |        12 | Multistart method for saem.mmkin models [21.6s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [3.7s]
+✔ |        15 | Plotting [4.6s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [66.1s]
+✔ |     1  36 | saemix parent models [30.9s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ────────────────────────────────────────────────────────────────────────────────
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.1s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.6s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [3.4s]
+✔ |        10 | Fitting the SFORB model [1.7s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         5 | Summary [0.2s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.6s]
-✔ |         9 | Hypothesis tests [6.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
+✔ |         5 | Summary
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.9s]
+✔ |         9 | Hypothesis tests [3.3s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 206.2 s
+Duration: 113.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 • This still takes almost 2.5 minutes although we do not solve ODEs (1)
 
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 267 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ]